niggle [nig-uh l ]
1 Cause slight but persistent annoyance, discomfort, or anxiety.
2 Criticize or annoy (someone) in a petty way
A trivial criticism, discomfort, or annoyance
After playing a cameo role for 10-man Colombia in a 2-1 opening defeat to Japan due to a calf injury niggle, Rodriguez returned to the fray for a decisive performance in their 3-0 win over Poland. (Tilbury, Michael, Pekerman: 'I'm extremely concerned' about possible Rodriguez injury, Chicago Tribune)
And with that, Louise had to be content. So why then, did a little niggle of doubt remain? (Rosie Goodwin, The Bad Apple)
Thank you for the clarification … this question has niggled at me for a long time. (Joan Morris, Are hummingbirds getting hypothermia from chilled nectar? Mercury News)
Early 17th century (in the sense 'do in an ineffectual way'): apparently of Scandinavian origin; compare with Norwegian nigla. Current senses date from the late 18th century. (Oxford English Dictionary)